Fig. 5

mRNA meta-gene profiles from eCLIP correspond to RBP regulatory roles. a (left) Each line indicates the presence (orange) of a reproducible DDX3X K562 eCLIP peak for 9162 mRNAs that are expressed (TPM > 1) in K562. Each gene was normalized to 13 5′UTR, 100 CDS, and 49 3′UTR bins (based on average lengths among expressed transcripts in K562 cells). (right) A meta-mRNA plot is generated by averaging across all expressed genes, with shaded region indicating 5th to 95th percentile observed in 100 bootstrap samplings. b Heatmap indicates peak coverage for 104 datasets (requiring at least 100 reproducible peaks and at least one meta-mRNA position with 5th percentile greater than 0.002). Color indicates the average occupancy, normalized by setting (blue) minimum value to zero and (yellow) maximum to one. Meta-mRNA profiles were hierarchically clustered and manually labeled. c Heatmap indicates pairwise correlation (Pearson’s R) between each pair of positions along the meta-mRNA in b. d Lines indicate average normalized peaks per bin for all RBPs in the indicated class. Shaded region indicates one standard deviation. e Heatmap indicates odds ratio of overlap between eCLIP datasets in (x-axis) indicated meta-mRNA cluster versus (y-axis) annotated RBP functions. See Additional file 3: Fig. S5d for significance